Dear all,

 

I have some problems with the analysis of the HumanHT-12 Chip from Illumina
and hope somebody can help me.

 

I have been analysing the data using the GenomeStudio Software until now.
Due to the fact, that some of the bead types are underrepresented on the
array, illumina implemented a so called “imputing function”. The Techsupport
told me that it would not make a big difference if the imputing function is
used or not.

While comparing the results using both methods (no imputing vs imputing), I
found that the “imputing  function” leads to more than twice as many
differentially expressed genes (167 vs 396). 

 

I was wondering, if there is any analog function or package implemented in R
& Bioconductor ?

 

Any kind of advice is welcome.

Thank you very much in advance!

 

Kind regards,

Stefanie

 

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Dipl.Chem. Stefanie Figura

Leibniz-Institut für Arterioskleroseforschung

Department Genetische Epidemiologie vaskulärer Erkrankungen

Domagkstrasse 3

48149 Münster

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